# cutadapt 1.14 

cutadapt -O 1 \
-f fastq \
--match-read-wildcards \
--times 1 \
-e 0.1 \
--quality-cutoff 6 \
-m 18 \
-o rep1.IP.umi.r1.fqTr.fq.gz \
-a AGATCGGAAGAGCAC \
-a GATCGGAAGAGCACA \
-a ATCGGAAGAGCACAC \
-a TCGGAAGAGCACACG \
-a CGGAAGAGCACACGT \
-a GGAAGAGCACACGTC \
-a GAAGAGCACACGTCT \
-a AAGAGCACACGTCTG \
-a AGAGCACACGTCTGA \
-a GAGCACACGTCTGAA \
-a AGCACACGTCTGAAC \
-a GCACACGTCTGAACT \
-a CACACGTCTGAACTC \
-a ACACGTCTGAACTCC \
-a CACGTCTGAACTCCA \
-a ACGTCTGAACTCCAG \
-a CGTCTGAACTCCAGT \
-a GTCTGAACTCCAGTC \
-a TCTGAACTCCAGTCA \
-a CTGAACTCCAGTCAC \
../01_umi_tools_extract/rep1.IP.umi.r1.fq.gz > rep1.IP.umi.r1.fqTr.metrics

cutadapt -O 1 \
-f fastq \
--match-read-wildcards \
--times 1 \
-e 0.1 \
--quality-cutoff 6 \
-m 18 \
-o rep1.IN.umi.r1.fqTr.fq.gz \
-a AGATCGGAAGAGCAC \
-a GATCGGAAGAGCACA \
-a ATCGGAAGAGCACAC \
-a TCGGAAGAGCACACG \
-a CGGAAGAGCACACGT \
-a GGAAGAGCACACGTC \
-a GAAGAGCACACGTCT \
-a AAGAGCACACGTCTG \
-a AGAGCACACGTCTGA \
-a GAGCACACGTCTGAA \
-a AGCACACGTCTGAAC \
-a GCACACGTCTGAACT \
-a CACACGTCTGAACTC \
-a ACACGTCTGAACTCC \
-a CACGTCTGAACTCCA \
-a ACGTCTGAACTCCAG \
-a CGTCTGAACTCCAGT \
-a GTCTGAACTCCAGTC \
-a TCTGAACTCCAGTCA \
-a CTGAACTCCAGTCAC \
../01_umi_tools_extract/rep1.IN.umi.r1.fq.gz > rep1.IN.umi.r1.fqTr.metrics
